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PLoS One. 2013 Apr 11;8(4):e60559. doi: 10.1371/journal.pone.0060559. Print 2013.

DomHR: accurately identifying domain boundaries in proteins using a hinge region strategy.

Author information

  • 1Department of Chemistry, Tongji University, Shanghai, China.

Abstract

MOTIVATION:

The precise prediction of protein domains, which are the structural, functional and evolutionary units of proteins, has been a research focus in recent years. Although many methods have been presented for predicting protein domains and boundaries, the accuracy of predictions could be improved.

RESULTS:

In this study we present a novel approach, DomHR, which is an accurate predictor of protein domain boundaries based on a creative hinge region strategy. A hinge region was defined as a segment of amino acids that covers part of a domain region and a boundary region. We developed a strategy to construct profiles of domain-hinge-boundary (DHB) features generated by sequence-domain/hinge/boundary alignment against a database of known domain structures. The DHB features had three elements: normalized domain, hinge, and boundary probabilities. The DHB features were used as input to identify domain boundaries in a sequence. DomHR used a nonredundant dataset as the training set, the DHB and predicted shape string as features, and a conditional random field as the classification algorithm. In predicted hinge regions, a residue was determined to be a domain or a boundary according to a decision threshold. After decision thresholds were optimized, DomHR was evaluated by cross-validation, large-scale prediction, independent test and CASP (Critical Assessment of Techniques for Protein Structure Prediction) tests. All results confirmed that DomHR outperformed other well-established, publicly available domain boundary predictors for prediction accuracy.

AVAILABILITY:

The DomHR is available at http://cal.tongji.edu.cn/domain/.

PMID:
23593247
[PubMed - indexed for MEDLINE]
PMCID:
PMC3623903
Free PMC Article

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